[2024-01-24 11:34:39,375] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:39,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:39,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference
[2024-01-24 11:34:41,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:41,325] [INFO] Task started: Prodigal
[2024-01-24 11:34:41,325] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9b9e8d9-9509-46f9-a7b7-27628667ce94/GCF_019134555.1_ASM1913455v1_genomic.fna.gz | prodigal -d GCF_019134555.1_ASM1913455v1_genomic.fna/cds.fna -a GCF_019134555.1_ASM1913455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:54,589] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:54,589] [INFO] Task started: HMMsearch
[2024-01-24 11:34:54,589] [INFO] Running command: hmmsearch --tblout GCF_019134555.1_ASM1913455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference/reference_markers.hmm GCF_019134555.1_ASM1913455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,871] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,914] [INFO] Query marker FASTA was written to GCF_019134555.1_ASM1913455v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,914] [INFO] Task started: Blastn
[2024-01-24 11:34:54,914] [INFO] Running command: blastn -query GCF_019134555.1_ASM1913455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference/reference_markers.fasta -out GCF_019134555.1_ASM1913455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,912] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,915] [INFO] Selected 15 target genomes.
[2024-01-24 11:34:55,915] [INFO] Target genome list was writen to GCF_019134555.1_ASM1913455v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,921] [INFO] Task started: fastANI
[2024-01-24 11:34:55,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b9e8d9-9509-46f9-a7b7-27628667ce94/GCF_019134555.1_ASM1913455v1_genomic.fna.gz --refList GCF_019134555.1_ASM1913455v1_genomic.fna/target_genomes.txt --output GCF_019134555.1_ASM1913455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,207] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,220] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:08,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:08,221] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	100.0	1466	1467	95	conclusive
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	99.9988	1464	1467	95	conclusive
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	78.0385	364	1467	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	78.038	385	1467	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	77.4296	324	1467	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	77.0938	284	1467	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	77.08	260	1467	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	77.0448	299	1467	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.8723	296	1467	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.6783	246	1467	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.2294	119	1467	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.1651	134	1467	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	75.9536	99	1467	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.836	195	1467	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.7944	199	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,222] [INFO] DFAST Taxonomy check result was written to GCF_019134555.1_ASM1913455v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference/checkm_data
[2024-01-24 11:35:08,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,266] [INFO] Task started: CheckM
[2024-01-24 11:35:08,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019134555.1_ASM1913455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019134555.1_ASM1913455v1_genomic.fna/checkm_input GCF_019134555.1_ASM1913455v1_genomic.fna/checkm_result
[2024-01-24 11:35:49,892] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:49,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:49,911] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:49,912] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:49,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019134555.1_ASM1913455v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:49,913] [INFO] Task started: Blastn
[2024-01-24 11:35:49,913] [INFO] Running command: blastn -query GCF_019134555.1_ASM1913455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88334267-bb8f-4308-8cca-04c4b1af113c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019134555.1_ASM1913455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:51,805] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:51,809] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:51,809] [INFO] Target genome list was writen to GCF_019134555.1_ASM1913455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:51,900] [INFO] Task started: fastANI
[2024-01-24 11:35:51,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b9e8d9-9509-46f9-a7b7-27628667ce94/GCF_019134555.1_ASM1913455v1_genomic.fna.gz --refList GCF_019134555.1_ASM1913455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019134555.1_ASM1913455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:06,994] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:07,020] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:07,020] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000013085.1	s__Rhodospirillum rubrum	99.9988	1464	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	conclusive
GCF_000284415.1	s__Pararhodospirillum photometricum	78.0486	363	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992075.1	s__Pararhodospirillum oryzae	78.0188	387	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	77.4085	270	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	77.4031	314	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	77.2858	318	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCF_902729435.1	s__Magnetospirillum sp902729435	77.1411	329	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	77.1406	324	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108475.1	s__Phaeospirillum fulvum_A	77.1382	283	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	77.1309	365	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	77.0989	318	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	77.027	261	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000442515.1	s__Phaeospirillum fulvum_B	77.0241	242	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.9668	230	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	76.8708	296	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858635.1	s__Telmatospirillum sp903858635	76.729	279	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	99.88	99.86	0.92	0.90	3	-
GCF_014205675.1	s__Novispirillum itersonii_A	76.6811	240	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Novispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.2906	309	1467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:07,022] [INFO] GTDB search result was written to GCF_019134555.1_ASM1913455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:07,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:07,025] [INFO] DFAST_QC result json was written to GCF_019134555.1_ASM1913455v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:07,026] [INFO] DFAST_QC completed!
[2024-01-24 11:36:07,026] [INFO] Total running time: 0h1m28s